Enhance JSON Comparison and Logging in `BokehSnapshotExtension.py`

[UTSAVS26]

The BokehSnapshotExtension.py file in pyopenms_viz/testing/ is responsible for handling Bokeh snapshot comparisons by extracting and validating JSON data from generated HTML files. However, there are some areas that could be improved to enhance accuracy, maintainability, and debugging:

Reasons for Improvement:

1️⃣ Inefficient JSON Comparison:

• The current method (compare_json) relies on direct key-value checks but does not effectively handle unordered lists.
• This can lead to false mismatches in cases where the structure is the same, but element order differs.

2️⃣ Uncontrolled Debugging Output:

• The function currently uses print statements for debugging.
• Switching to Python’s logging module would allow better control over verbosity levels.

3️⃣ Lack of Unit Tests:

• There are no dedicated tests to verify Bokeh snapshot extraction and comparison.
• Adding tests using pytest and syrupy will improve reliability and prevent regressions.

4️⃣ Potential for Enhanced Serialization:

• Right now, only HTML is stored, but supporting raw Bokeh JSON snapshots could improve performance and debugging.

These improvements will make Bokeh snapshot testing more accurate, maintainable, and easier to debug. I would like to work on these changes to enhance the robustness of snapshot testing in the project.

[jcharkow]

Thank you for taking the initiative and identifying this issue. I agree the BOKEH snapshot extension definitely needs improvement, is hard to read and is buggy and not currently tested. You are welcome to tackle this issue however some of the issues highlighted above might not need addressing. Please see comments below.

See comments below:

1. Please provide an example where unordered lists would be needed in the BOKEH JSON comparison as I am not sure if they are used. From my understanding it seems that BOKEH mostly uses dictionaries which are handled by the current lists.
2. What would be even better is to switch to modify syrupy's/pytest output. Currently when a test fails, giant strings are produced which are hard to decipher as a user. Configuring the print statements to work with pytest/syrupy better would be an asset. Unfortunately, I don't know what steps would be required to address this so you would have to take initiative on this project.
3. Yes good idea! Feel free to add this for matplotlib and plotly backends as well!
4. I specifically chose to use html rather than json because I like that you can easily open and visualize the HTML file in a browser. Plotly has a mechanism to plot straight from the plotly json however I was not able to find this for bokeh and that's why I chose to stick with HTML. Also it seems that json is stored in the html file so that is what is used currently.
   • Having said that if you find a way to store both the .html and the .json for bokeh than I would be open to switching to json.

[UTSAVS26]

Thanks a lot for the feedback! I really appreciate your thoughts, and I’ll make sure to address everything. Here’s my take on your comments:

1. Unordered Lists in JSON:
   I get what you're saying about Bokeh mostly using dictionaries. I’ll take another look at the JSON structure to double-check if there are any unordered lists. If there are, I’ll adjust the code to handle that. If not, I’ll focus on improving the comparison for dictionaries only as you mentioned.

2. Debugging Output:
   I agree, using print statements isn’t ideal. I’ll switch to Python’s logging module to give us more control over the verbosity. I’ll also look into how we can configure the output to work better with pytest and syrupy to avoid those long, hard-to-read error strings when tests fail.

3. Raw JSON and HTML Files:
   I totally see why you prefer using HTML - it’s much easier to view in the browser. I’ll explore how we can store both the HTML and the raw JSON for Bokeh to see if it’s helpful. If it is, I’ll make a plan to handle both formats for testing.

4. Unit Tests:
   Adding unit tests sounds like a great idea! I’ll work on adding tests with pytest and syrupy to make sure the snapshot extraction and comparison are solid and don’t break in the future.

Thanks again for all your input. I’ll get started on these changes and keep you updated as I go!

[UTSAVS26]

Hello @jcharkow sir,
I wanted to inform you that I have raised a dedicated pull request (PR) for the issue at hand. Whenever you have the time, could you please review it?

Thank you for your attention to this matter.